Because gemstones form under unique circumstances, each individual gemstone is comprised of a combination of trace minerals, which create a unique set of identifying marks or inclusions. Inclusions will not necessarily detract from the beauty or desirability of a colored gemstone.
When considering a colored gemstone's clarity, you should measure your expectations against the standard for that variety of gemstone. Some varieties of colored gemstones, such as aquamarine, blue topaz, and citrine, have naturally fewer inclusions while other gemstones, such as emerald and ruby, tend to have a higher rate of acceptable inclusions.
Clarity is an important factor in comparing quality colored gemstones. Even opaque opals can have milky inclusions that will affect their iridescence and color play. In general, the best values are available in gemstones that are moderately included. Exceptional gemstones with few or no inclusions are available, but they can command extravagant prices.